Transactivation Response RNA Binding Research Articles

The interferon-induced protein kinase R: the base of a riboprotein scaffolding regulating the human immunodeficiency virus.

The interferon-induced RNA-activated Protein Kinase (PKR) targets the alpha subunit of the eukaryotic translation initiation factor 2 (eIF2α) whose phosphorylation blocks translation initiation of cellular and viral mRNAs. PKR is activated at the beginning of human immunodeficiency virus (HIV) infection by low levels of the HIV Transactivation Response (TAR) RNA and by the cellular PKR Activator (PACT), which contributes to a reduced viral replication. During HIV replication, the viral Tat protein and high production of TAR RNA decrease PKR activation. The cellular TAR RNA Binding Protein (TRBP) and Adenosine Deaminase Acting on RNA (ADAR1) also prevent PKR activation, while HIV expression changes PACT function to become a PKR inhibitor. Therefore, HIV recruits viral and cellular factors to counteract PKR antiviral activity. In addition, PKR antiviral function was positively selected during evolution due to contacts with viral factors inhibiting its function. The riboprotein scaffolding such as the one that inhibits PKR during HIV replication may exist for other antiviral factors.

The interferon-induced protein kinase R: the base of a riboprotein scaffolding regulating the human immunodeficiency virus.

The interferon-induced RNA-activated Protein Kinase (PKR) targets the alpha subunit of the eukaryotic translation initiation factor 2 (eIF2α) whose phosphorylation blocks translation initiation of cellular and viral mRNAs. PKR is activated at the beginning of human immunodeficiency virus (HIV) infection by low levels of the HIV Transactivation Response (TAR) RNA and by the cellular PKR Activator (PACT), which contributes to a reduced viral replication. During HIV replication, the viral Tat protein and high production of TAR RNA decrease PKR activation. The cellular TAR RNA Binding Protein (TRBP) and Adenosine Deaminase Acting on RNA (ADAR1) also prevent PKR activation, while HIV expression changes PACT function to become a PKR inhibitor. Therefore, HIV recruits viral and cellular factors to counteract PKR antiviral activity. In addition, PKR antiviral function was positively selected during evolution due to contacts with viral factors inhibiting its function. The riboprotein scaffolding such as the one that inhibits PKR during HIV replication may exist for other antiviral factors.

Multiple levels of PKR inhibition during HIV‐1 replication

Recent therapeutic approaches against HIV-1 include IFN in combination therapy for patients with coinfections or as an alternative strategy against the virus. These treatment options require a better understanding of the weak efficacy of the IFN-stimulated genes, such as the protein kinase RNA-activated (PKR), which results in viral progression. Activated PKR has a strong antiviral activity on HIV-1 expression and production in cell culture. However, PKR is not activated upon HIV-1 infection when the virus reaches high levels of replication, due to viral and cellular controls. PKR is activated by low levels of the HIV-1 trans-activation response (TAR) RNA element, but is inhibited by high levels of this double-stranded RNA. The viral Tat protein also counteracts PKR activation by several mechanisms. In addition, HIV-1 replicates only in cells that have a high level of the TAR RNA binding protein (TRBP), a strong inhibitor of PKR activation. Furthermore, increased levels of adenosine deaminase acting on RNA (ADAR1) are observed when HIV-1 replicates at high levels and the protein binds to PKR and inhibits its activation. Finally, the PKR activator (PACT) also binds to PKR during HIV-1 replication with no subsequent kinase activation. The combination of all the inhibiting pathways that prevent PKR phosphorylation contributes to a high HIV-1 production in permissive cells. Enhancing PKR activation by counteracting its inhibitory partners could establish an increased innate immune antiviral pathway against HIV-1 and could enhance the efficacy of the IFN treatment.

Zinc finger-dependent HIV-1 nucleocapsid protein-TAR RNA interactions.

In the minus-strand transfer step of HIV-1 reverse transcription, the nucleocapsid protein (NC) promotes annealing of the 3' 'R' (repeat) region of the RNA genome to its complementary sequence located in the newly synthesized minus-strand strong-stop DNA. The R region contains the highly stable transactivation response (TAR) RNA hairpin. To gain insights into the molecular details of TAR RNA-NC interactions, we carried out hydroxyl radical footprinting, as well as gel-shift and fluorescence anisotropy binding assays using wild-type and mutant forms of NC. Our results support the conclusion that NC variants with mutations in their zinc finger domains have dramatically altered TAR RNA binding interactions relative to wild-type NC. These data demonstrate that a specific zinc finger architecture is required for optimal TAR RNA binding, and help to explain the requirement for the zinc finger motifs of NC in its role as a nucleic acid chaperone in minus-strand transfer.